0.4.4: 3.8 support, min_depth defaults to 1 in CLI & API, setup.py tw…

…eaks

.travis.yml

@@ -7,6 +7,7 @@ language:
 python:
   - 3.6
   - 3.7
+  - 3.8
 before_install:
 - sudo apt-get install samtools
 install:

kindel/__init__.py

@@ -1 +1 @@
-__version__ = '0.4.3'
+__version__ = '0.4.4'

kindel/cli.py

@@ -11,7 +11,7 @@
 
 def consensus(bam_path: 'path to SAM/BAM file',
               realign: 'attempt to reconstruct reference around soft-clip boundaries'=False,
-              min_depth: 'substitute Ns at coverage depths beneath this value'=2,
+              min_depth: 'substitute Ns at coverage depths beneath this value'=1,
               min_overlap: 'match length required to close soft-clipped gaps'=7,
               clip_decay_threshold: 'read depth fraction at which to cease clip extension'=0.1,
               mask_ends: 'ignore clip dominant positions within n positions of termini'=50,

kindel/kindel.py

@@ -354,7 +354,7 @@ def consensus_sequence(weights, clip_start_weights, clip_end_weights, insertions
 
 
 def consensus_seqrecord(consensus, ref_id):
-    return SeqRecord(Seq(consensus), id=f'{ref_id}_cns')
+    return SeqRecord(Seq(consensus), id=f'{ref_id}_cns', description='')
 
 
 def build_report(ref_id, weights, changes, cdr_patches, bam_path, realign, min_depth, min_overlap,

setup.py

@@ -1,5 +1,4 @@
 import re
-import sys
 
 from setuptools import setup
 
@@ -8,10 +7,6 @@
                         open('kindel/__init__.py').read()).group(1)
 
 
-if sys.version_info[0] < 3:
-      sys.exit('Kindel requires Python >= 3.6')
-
-
 CLASSIFIERS = ['Environment :: Console',
                'Environment :: MacOS X',
                'Intended Audience :: Science/Research',
@@ -21,18 +16,20 @@
                'Operating System :: MacOS :: MacOS X',
                'Programming Language :: Python :: 3.6',
                'Programming Language :: Python :: 3.7',
+               'Programming Language :: Python :: 3.8',
                'Topic :: Scientific/Engineering :: Bio-Informatics']
 
 
 setup(name='kindel',
       version=__version__,
-      description='Indel-aware consensus calling for DNA alignments in BAM format',
+      description='Indel-aware consensus calling for nucleotide alignments in BAM format',
       url='https://github.com/bede/kindel',
       author='Bede Constantinides',
       author_email='bedeabc@gmail.com',
       license='LICENSE',
       packages=['kindel'],
       zip_safe=True,
+      python_requires='>=3.6',
       install_requires=['argh>=0.26.2',
                         'tqdm>=4.11.2',
                         'numpy>=1.12.0',